Tuesday, November 30, 2004

Tick...tick...tick...

It has been nearly four weeks since the manuscript went away and we still have not heard back. The first two weeks were relatively lighthearted, but now I'm starting to crawl backwards out of my skin. It's really hard to enjoy the planning and looking forward, the exciting part of science, without knowing how the other shoe will drop. And A LOT is hanging on how well this goes. Jennifer asked me what if the manuscript is rejected. I said, I don't think that way; jokingly adding-- just like I didn't think Kerry would lose. But I'm now notthinking as hard as I can.

... Nature never did betray
the heart that loved her; 'tis her privilege,
through all the years of this our life, to lead
from joy to joy; for she can so inform
the mind that is within us, so impress
with quietness and beauty, and so feed
with lofty thoughts, that neither evil tongues,
rash judgements, nor the sneers of selfish men,
nor greetings where no kindness is, nor all
the dreary intercourse of daily life
shall e'er prevail against us, or disturb
our cheerful faith, that all that we behold
is full of blessings.

Wordsworth

I hope She's out there now.

Hiding your motives

I'm a little nervous about how visibly a fascination with science fiction and fantasy worlds has permeated the internet science community. This side of the science world was supposed to be a closely held secret that thousands of pimply-faced, virgin boys supressed from view in order to.. ahem...well, to get on with things.
In the last two months I have caught two serious reviews now discussing Star Trek in the context of extraterrestrial life. Via The Eternal Golden Braid , professor Stephen Brenner speculates that maybe extraterrestrial life doesn't need liquid water, especially at very low temperatures, which would definitely upend a lot of the criteria used now to narrow the search. To bolster his arguments, he cites several life forms encountered by the Star Ship Enterprise in their five-season quest for sequels. A while back, a Chris McKay review on the same topic also pined for the famous "tricorder" which could detect life at a distance. Now Gene Rodenberry, may his ashes never waft into my coffee, was a brilliant man, but I think I'm not ready yet to footnote him.

Full disclosure: author has viewed Star Wars episode IV in excess of 100 times, and can recite long stretches of Monty Python from memory. Author has kissed a girl.

Monday, November 29, 2004

Mmmmmmm.....

Stolen from Hit and Run : Mark Steyn's eulogy for Bill Mitchell, the inventor of Cool Whip.


Mary Vermette’s excellent “Pudding Dessert” requires for the first layer 2 sticks of oleo, 2 cups of flour, 1 cup of chopped nuts (mix and bake); for the second layer, 1 cup of confectioner’s sugar, 8 oz of cream cheese, 1 cup of Cool Whip (combine and spread on the first layer); for the third layer, 2 small packages of instant pudding and 2 ½ cups of milk (mix and spread on the second layer); and for the fourth layer more Cool Whip sprinkled with chopped nuts. I made it and ate it in the interests of research, and had such a good time I clean forgot what it was I was meant to be researching. (Mark Steyn)

Eye on Ukraine

Daniel Drezner has a discussion of the escalating crisis in the Ukraine. There is much more going on than a fraudulent election- both candidates have big centers of support, and now both have lined up heavy hitters on the outside. I think there is a good chance of an outbreak of violence. It looks like no one at the top wants civil war, but let's just keep fingers crossed.

Hobbit trouble

Via the excellent science site The Loom , a disturbing development with respect to the Homo Floresienis remains found in Indonesia. These small skeletons appear to be non-homo sapiens, but the remains are only about 20,000 years old, suggesting that modern humans overlapped chronologically with their close cousins for a very long time.
Unfortunately, the remains have been "taken into custody" (subscription link) by a politically connected anthropologist in Indonesia.
The condition of the remains was already very sketchy (I think the reports out of Nature said the preserved bones had the "consistency of soap") and, as Carl points out, if mitochondrial DNA retrieval is to work then the remains have got to be kept scrupulously clean of modern human contamination. Even a fingerprint could throw the analysis.
As there is still some doubt that these remains are not modern human (possibly pygmy), it would be critical to safeguard the original sites and give access to the existing remains-- and soon!

Saturday, November 27, 2004

My son, the next Tom Sawyer

McDonald's in Germany is giving out little boom boxes with their Happy Meals. You get different colors, of course, and each one plays a little clip from a Germlish rock band. My son sings along, generating a total cultural mishmash-- a bilingual kid misquoting a warbling toy emitting crap lyrics sung by a German imitating an American-- all courtesy of McDonald's Deutschland. Garbage in, garbage out, but what happens if you loop the garbage out back in?
The boys got different colors, and somehow the older one convinced the younger one that it would really be better if he had them both for the day. This in the name of "sharing." At dinner last night, I began the cross-examination.

--So, what happens tomorrow? Matthew, the younger, tells me: Each kid gets one.

--But what do you get for a trade? Matthew is irritated that I don't understand: The trade is, I get to have my boom box back.

--But don't YOU get any privilege? Josef, my Tom Sawyer-in-training, looks a little uncomfortable, but Matthew is adamant: It's very easy Daddy. First, Josef gets it. Tomorrow, I get it.

Game, set, match.
By the way, Josef still hasn't given it back this morning.

Friday, November 26, 2004

Stem cells and specific cancers

In the last two weeks there have been additional reports of abnormal stem cell behavior resulting in specific types of cancer. Stem cells are of therapeutic interest because they are able to give rise to very many cell types- skin, muscle, you name it-- and with the right growth conditions they can continue to propagate for a long time. It is best understood how to isolate stem cells from embryos, but there is increasing attention to stem cell populations in adult bodies. One could foresee a day when stem cells could be isolated from an adult's healthy tissue, grown up, and then given back to that same person. But the potential and drawbacks are not fully known!

These papers highlight the idea that studies in stem cell biology may improve understanding of the earliest events in some cancers as well. Go California!!!!

The studies in the last week are all in Science and Nature and are behind subscription walls. This is a very interesting topic to me, so I will try to get out a public-access set of links soon.
So here are the links:
The lab of Tim Wang will have an article on gastric cancers arising from circulating Bone Marrow derived Stem Cells (BMSCs), to appear in Science this week. (subscription link here )
Phil Beachey et al. have written a review highlighting Wnt and Notch abnormalities in cells repairing injured tissues, and hypothesize possible derangement of the repair response in cancer stem cells in the November 18 Nature. (free link here ; Subscriber link is here .)
Singh et al., studying human brain glioblastomas, give evidence that these tumors originate as CD133+ brain stem cells. This work is in the same issue of Nature. (free link here and News and Views here )

Wednesday, November 24, 2004

Mars Express images of Huygens crater

110-280904-0532-6-co-01-HuygensRim_l
The Mars Express mission of the European Space Agency has released new processed images of Huygens crater on the southern hemisphere of Mars. The huge crater, taking up the whole bottom edge of the photo (see the scalebar at the top!), is about 1 bilion years old and has been partially filled with sediments. Check out the darker "dendrites" feeding into the secondary craters! These look just like desert drainages.

Many more images, including rotated and profile views, are here . Fantastic!

The next Bill Gates

Via The American Prospect , a fantastic article by Fareed Zakaria (Washington Post, subscription required) about how increased U.S. visa restrictions are reducing the flow of researchers into the U.S. from abroad. Zakaria urges Condoleeza Rice to revise the current visa guidelines, which have become much more strict in the wake of September 11th. We want to keep out the next Mohammed Atta, but let in in the next Bill Gates.
In the fairly large molecular biology lab where I did my Ph.D., there were 12 postdocs, but only two had been born in the U.S. American-borns were more numerous among the graduate students, but I have seen other institutions where foreign students were in the majority. Quite often these postdocs and students sought to complete their careers in the United States, which amounted to a terrific profit for the U.S. at the expense of whichever country which gave the university training. Zakaria quotes the National Science Board that 38% of science and engineering doctorate holders are foreign born. If we raise the immigration bar on these people too high, they'll just go somewhere else and power some other nation's research institutes.

Zakaria gives pretty short shrift to the balance of these values against security concerns. One of the creepiest revelations from the early days after 9/11 was that Mohammed Atta and others had lived with American families in Florida while attending flight training school. I remember wondering if Americans would therefore think twice before showing kindness to some other immigrant student. The point is, how could you possibly know? The border remains the correct place to try to make that distinction. And I think the job is pretty near impossible.



Any ideas out there?

UPDATES: Yes, I know Bill Gates was born in America, as were others, including me.

Check out the McKinsey-style bullet point presentation of Winning Argument on this. Must one always be either right or wrong? Anyway, some good links.

Tuesday, November 23, 2004

The worst jobs in science

This years' Worst Jobs in Science include a Landfill Monitor and an ecologist at the heavily polluted St. John's Harbor. Makes it feel pretty comfy at this desk....

Monday, November 22, 2004

Methane on Mars

Results presented The American Astronomical Society's Planetary Sciences meeting in Louisville earlier this month confirmed and strengthened the case for methane on Mars. Compounds like methane should be very unstable in the Martian atmosphere, indicating that something has been producing large amounts of methane up until the very recent past, or even continuing today. On earth, methane is chiefly produced by vulcanism and by the actions of so-called methanogenic Archea. At least one scientist involved in the recent work thinks that "oases" of living methanogen colonies could explain the observations on Mars. Methanogens "breathe" hydrogen gas and CO2 and "exhale" methane, all without oxygen.

With all of these ideas, of course, one must keep in mind that the whole planetary history of Mars is different from Earth, so all bets are still off! Still, the amounts of methane, and their apparently patchy distribution are going to be hard to explain. Moreover, the huge dust storms seen on Mars should be kicking up lots of surface soil. These soils contain oxides, which also can degrade methane, possibly "sweeping" parts of the atmosphere clean of methane on a much more rapid time scale-- months?-- even than currently discussed. In that case, something is really pumping the gas out!
An important second measurement which would strengthen the case for life on Mars would be the relative absence of ethane, which is released by geological processes which produce methane, but not by (terrestrial) methanogenic Archaea. Even an abiotic source of methane is likely to be a source of heat and therefore liquid water, so it will also be important to find out where the stuff is coming from!

UPDATES: I got the methanogenic metabolism wrong- it's 4H2 + CO2 making 2H20 plus CH4. I corrected this in the text above. This is a problem because free hydrogen should not be hanging around on Mars, and would have to be generated for these beasties to eat. On earth, many methanogens are hyperthermophiles; however, the "cow fart" variety lives at, well, cow temperature.

And the New York Times has a big and informative article.

Saturday, November 20, 2004

Elections technology

I have spent a lot of time in the last weeks explaining how elections work to fairly incredulous European co-workers. It's hard for them to believe that there is not a national standard for voting technology, let alone that voter participation is as low as it is in the U.S. Although I feel that this election went off without spectacular technological glitches, I think this is going to come back and haunt us.
Our president has become the most important person in the world, and presidential elections deserve the most secure, reliable possible voting technology AND the highest possible voter participation.
In that light I was interested to read this article from Commondreams.org. The author actually believes that election fraud occurred in Florida, and I have to state that I do not agree. Nevertheless, the six suggestions make sense to me. The most important of all is, why cannot elections fall on a holiday? They are held on Sunday in Germany (which is officially Christian, so Sunday is everyone's day off) and I am sure that it would help keep lines down and help more people volunteer to keep the poll stations moving.
The second suggestion I agree with is that same-day voter registration should be allowed-- with certain very limited, but non-negotiable, sets of identification, i.e. driver's license or passport olus evidence of residence. You either have it or you don't, 30 second decision, shooting for 90% positive. In principle I don't mind scrutiny of earlier registration applications, but the trade-off should be that more than one kind of evidence would constitute proof of eligibility.
As to voting technology, I have seen a lot of support for good old pen-and-paper. But also check out this thread from slashdot.org.

Friday, November 19, 2004

Speaking of databases

Check out this link from Jeff Jarvis describing how the Republican party approached voting like a consumer question: which groups are likely to buy our product, and how can we reach them? They built up a database and bought advertisements timed to reach the people they thought they needed to. It seems very simple, but you can't argue with success.

Google Scholar

Google has a new search engine which is intended for more academic use compared to the all-purpose regular Google. In my business, we rely a lot on Entrez-Pubmed , which is maintained by the public National Center for Biotechnology Information. But just regular Google is often so powerful that I look for additional information using that database as well.
So I clicked on over and typed in a few searches. The first thing I noticed was that most of my hits were research articles. In fact, many of the links for older articles seemed to lead right back to Entrez-PubMed, making me think that even as Microsoft is picking Google's pocket, Google's robots are busy at the NCBI.

The second thing I noticed, which I think is a possible improvement over PubMed, is that the Google hits tell you how many times a given link has been further cited. I have described in the past how young faculty live or die based on the scientific citation index of the journals in which they publish. It looks to me that Google has an independent way of measuring how important an article is in the internet world. This could get interesting....

So all in all, I'm pretty impressed. I do think I'll use it in my daily work, as it seems to cast a broader net than PubMed. I will miss the sort of oddball hits that come up with a conventional Google search though.

I showed two or three of my colleagues and they're all searching for their own names(I'm also guilty!)

The dry limit of life

People interested in the possibility of life outside of earth spend a lot of time thinking about liquid water. Compared to the other requirements of Earth life, such as energy sources and complex organic chemistry, liquid water is very rare in the solar system. Moreover, in terrestrial life, liquid water is chemicallly involved in the synthesis of the building block molecules DNA, RNA, and proteins, and helps transport nutrients and wash away wastes.
This focus on liquid water is the reason for the magnesium sulfate geology work on Mars, and the attention to possible ice volcanoes on Titan.
I should emphasize out that Mars is VERY dry, and Titan VERY cold, so the evidence for liquid water in both locations should be viewed with the perspective that we're still talking about conditions more extreme than seen anywhere on Earth.

But how dry is too dry? Scientists have thought the absolute desert region of the Atacama desert in Chile, which receives rain as infrequently as once a decade, to be devoid of life (subscription to Science required). Now a team led by RM Maier at the University of Arizona has successfully cultured bacteria from subsurface samples in even these extremely dry regions. The authors speculate that they may have managed to find these bacteria by digging about 20 cm deeper than prior investigators.
The Viking missions to Mars in the middle seventies tried to look for life by a couple of means, but found only oxides in the surface soil. Oxides are rapidly destroyed by water, suggesting the complete absence of water in the soils tested by the Viking landers. This oxide chemistry was also found in the surface soils in the Atacama desert(see the Science link). Thus, the potential significance of the new Atacama desert findings are that even when surface soils show extreme dessication, nevertheless living things can be hanging on just a little bit deeper.
So, with the caveat that Mars conditions are still more extreme than seen even in the Atacama, we can say that we don't yet know how dry is too dry. Let's keep looking!

Monday, November 15, 2004

Astrobio site from NASA

I was just looking around to see if something has been happening with the Cassini imaging of Titan (nothing obvious) when I saw that NASA has a separate astrobiology page . This site looks really full of goodies!
I clicked onto the headliner, Water from a stone and had a look. Scientists looking for evidence of (past) life on Mars need information about the climate and water history of a particular spot. A promising source for this kind of local information would be as the magnesium sulfate deposits observed by the Viking and later missions. Magnesium sulfates can retain varying amounts of water in their alternative crystal structures. In fact, the relative abundance of different crystal forms of magnesium sulfate is a sensitive indicator of how humid conditions were at the time of the rocks' formation. However, that same sensitivity makes it very difficult to transport these minerals back to Earth without risking transformation between forms or amorphization (loss of crystal structure), driven by the humidity and pressure in transit. To avoid this risk, the scientists would like to equip a future mars lander with an X-Ray diffractometer, which can distinguish the various forms of magnesium sulfate on rocks right on site. Finding a combination that suggests (relatively) warm and wet formation conditions would highlight that locale as a place to search for evidence of life.

I think right now the smart money's on bacterial forms buried well below the surface, where they would be/would have been shielded from temperature extremes and radiation, and might have/have had access to water reservoirs.

As a molecular biologist, I just want to see if those extraterrestrial beasties have DNA! Does anyone else think it's cheesy that almost every character in Star Wars has two eyes and two nostrils? Even Jabba the Hut has a face and a dorsal spinal cord, meaning his ilk has neural crest cells just like earth vertebrates. Hmmmm.... better than Star Trek though.

Pop-tarts and beer.

Ok, now that I have your attention, I would like to talk about data management. Yesterday's New York Times discusses Wal-Mart's predictive technology, in which they mine past sales records to anticipate purchase surges in specific items. The unexpected result for an oncoming hurricane was that Pop-tarts sell at about 7 times their normal rate. After that, beer is a no-brainer. What else would you use to wash down the Pop-tarts? Calling Dave Barry...

I went through the whole article, and I think something is strangely missing. Yeah, Wal-Mart has mountains of data, and they use that information to stock products and to admonish suppliers, but at what point is this different (except in scale) from the corner grocer? Moreover, a lot of other big retailers are also collecting and mining data. Why is Wal-Mart so successful relative to them? I still don't know. However, data-based predictive approaches can be hugely effective in many settings, as David, Joanna and Marcy can all attest!

Lastly, the article mentions customer's privacy concerns. This section of the article was especially brief and vague. Since Wal-Mart apparently tracks products and shopping carts, not identified customers, it may be that concerns about linking e.g. credit history with particular profiles did not belong in this article. Other retailers with loyalty card systems are far more interested in knowing all about you. This is a very complex issue, and deserves better discussion than I can manage. I do have to say that the genie is already out of the bottle, and that information, once given out, will no longer be erased or forgotten.

Thursday, November 11, 2004

Blink, and you'll miss it

We had our first real cold snap this week, and a little bit of snow. It has been wonderful biking in the woods to work. The coming of winter helps me forgive Munich for its dreary long fall.
I turn off my headlamp (it's dark already at 6PM) and bike hrough the woods in snowlight, using the black of the trail against the snowy edges. The trees had not yet lost their leaves before this week's snow, so they bend down snow-arms across the trail.

It's absolutely silent in the woods. It seems hard to believe I'm living at the edge of a city of 3 million. Astonishing.

The boys got their new snow things this week, which instantly doubles the time we need to get out the door. Our youngest, Geordie, has outgrown the plaid snowsuit that all three boys had worn. That's it-- it's done! We'll never use that suit again. It was an ugly old thing, but it sure kept them warm. He's in a sporty new REI outfit that grandma bought. Josef and Matthew are also wearing new coats and new hats. Matthew's has a pompom, which he refers to as his "alarm." During the flurries yesterday, he bared his cheek and asked me if he had snow freckles. A poet could do worse than riffing on his kids' neologisms.
Last night after bedtime, there was some definite noncompliance going on. I went up for a look-see, and glimpsed Matthew flopped on his bed, head propped up on elbows, flipping through a comic book like a teenager.

Having young kids around makes you appreciate how quickly life can move. They go about their lives with seeming nonchalance, but you put them into a new coat, and they suddenly look years beyond your laggard preconceptions. I guess this help keep you young at heart, because they deliver moments like this of complete astonishment. But keep on your guard, because they're chary with their revelations. Blink, and you'll miss it.

Tuesday, November 09, 2004

Mapping up

Take a look at this link showing 2004 presidential election result cartograms using different metrics. When corrected for voter densities, Florida still looks like a big red-- well, never mind. Lots of red out there. Lots of mappers are tinting things purple to make the blue states look less isolated. The point is, this election divided sharply but it doesn't have to be that way.

Meanwhile, Gary Hart jumps the shark , saying politicians oughta keep quiet about their religious beliefs. Dude, that is so 48 hours ago. Gary's a really smart guy, and should be a voice on the left for the hearts-and-minds side of keeping terrorism in a cage. But blaming religion for the election results at this point is, first of all, spitting into the wind, but also just going to drive undecideds away.

Monday, November 08, 2004

Spirit rover on Mars

The Spirit rover is still plugging away on Mars and has nearly left the Gusev crater. The preliminary overall picture of the geology near the Spirit landing site is emerging. Most of the layered rocks appear to have originated as volcanic ash, with very prominent water action pulling out the salts from the ash. The rover might be able to figure out if the water erupted with the minerals or if it was supplied separately.

On the whole I think this region is not so promising for essentially fossil hunting. What you would have wanted to see would be a nice layered sandstone. Volcanic ash itself is very likely to be pretty sterile, so all the water in the world couldn't help something live there. Still, a lot hangs on where exactly the water came from.

Medium Dad

Well we never made it to the pool yesterday. We headed out in good spirits, but unfortunately too close to lunchtime. Then we missed the first bus, and sat parked in the next one until the 20 minutes had gone by.
The trouble really started at the connection, which should have been about 15 minutes. It was raining and cold, and it was crowded in the tiny bus shelter. My older son was hungry, and he ate his sandwich and half of mine, and Matthew also ate all of the salami slices. But they were bored, and started wrestling each other, and I had to keep telling them to settle down. 30 seconds' peace, then wrestling again, then another warning. Quiet, then more squabbling. Still no bus.
Finally they started bickering over the kickboard and I finally pulled the plug, and we headed back. The boys protested, but I had had it. The connection bus arrived just as we left. On the return trip Josef burst into tears and Matthew was pretty hostile. I really hate seeing Josef cry. I was having second thoughts, but as the rain turned to sleet, I imagined trying to get them home after two hours' splashing around.

I managed to make peace with Josef by making hot cocoa with cinnamon. Within 20 minutes they were upstairs playing. I think I was the only one still feeling bad about the missed chance.

We started butting heads again at bathtime. They have a game involving tigers, dinosaurs, superheroes and quite a lot of splashing. More warnings about confiscating toys. I left the bathroom and I overheard Matthew: "we sure have a mean Daddy."

Josef thought for a minute. "No, just medium."

Sunday, November 07, 2004

Lazy days

We're just staying around the house this weekend. The manuscript went off on Thursday, so Monday I'll start up the CYA experiments. In the meantime I just want to hang around, get the last election toxins out, and be with the boys. The weather has been very cool and even a bit rainy today, so I think we're going to head over to one of Munich's massive indoor pools.

I have been following the story of Arafat's illness and the impending strike on Fallujah, but not with anything like my pre-election interest. Regnum Crucis has a well-spoken Red State perspective on the election and the subsequent liberal dissections of what happened. All I would say is that the misconceptions--and real anger-- seem to have been going in both directions. Not good for a country at war. My main feeling about the election was that it was 75% about committed party identity-- a replay of election 2000-- and the deciding 25% was about all sorts of things including differences in deeply held moral convictions. The stoking of those convictions was electorally potent, but does make people of different beliefs a little bit nervous. Again, not good for a country at war. Mission accomplished.

And anyway, it doesn't make it suck any less.

Also a few science stories. The flyby of Titan seems not to have resolved what exactly the Huygens probe is going to land on (or splash into) in when it falls to the surface near Christmas time. I am trying to get a post together about the significance of liquid water in exobiology (and why therefore Titan is of secondary interest compared to Mars or Europa). Titan is basically Los Angeles on ice, with smog in the air and tar pits on the ground. No possibility of life there.

There was a story two weeks ago about giving fluoxitene (Prozac) to mice with advanced pregnancies. Their offspring subsequently score very high on anxiety tests. I have not yet gone to the paper, but my instincts are that this will fall in the realm of the Aspartame and bladder cancer tests in rats- wrong dose for too long a time, human medical implication uncertain.

Friday, November 05, 2004

More marginal thinking

Once more emphasizing that the election was mostly about committed "fortress red" voters flexing on "chateau blue" states, I just wanted to link to one or two more commentators.

Matthew Yglesias is on an absolute roll.
Jim Henley also talks quite a lot about the debacle of losing even though Bush basically gave up the center. Money quote:

".... it appears that the Republicans will have won thanks to their direst characteristics, reifying of the national security state and codifying the moral outlook of a particular slice of Christendom into law. And the Democrats will have lost thanks to their equivocal stands against promiscuous war and for civil liberty - their best characteristics. I can envision some good things coming from Bush II, and some bad things not happening that would have happened under Kerry. But on balance this is a bad election to be a libertarian."

I do have one issue with his analysis. He claims the wooing of the "morality" vote of one of the undecided groups was all done sub rosa. C'mon! Karl Rove was saying "Guns, Gays, God" for a whole year! I think instead it was not taken seriously by the circle of people I read. (I was blindsided as well.)

Rove didn't disguise this strategy at all, which incidentally I regard as curious, to put it mildly, for a self-described fan of the Federalist Papers.
Note to self: it's not considered pandering if it works.